He should never have been down there endangering spock's life in the first place, and though morally it was the right thing, he did alter the natural development of the Nibiru native population, and broke Starfleet's #1 directive of not interference.

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There is no further development period without the interference.

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Yeah, Spock's preaching to Kirk about violating the prime directive made no sense, because Spock was doing the same thing by stopping the volcano!!

Like Pike said, they were there to OBSERVE.

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Yes, but if Kirk didn't pull the Enterprise out of the water, the aliens wouldn't have known why the volcano stopped.

They were already violating the prime directive, but it was a clear violation once they exposed the ship.

Remember..this is all an alternate reality so all we know about Starfleet and the people are all brand new and the old stuff we know can be thrown out. Anything goes and we are establishing new canon here.